def load_population_data(self, population):
"""Load node properties from SONATA Nodes.
Args:
population (str): a population name .
Returns:
pandas.DataFrame with node properties (zero-based index).
"""
nodes = self.storage.open_population(population)
categoricals = nodes.enumeration_names
node_count = nodes.size
result = pd.DataFrame(index=np.arange(node_count))
_all = libsonata.Selection([(0, node_count)])
for attr in sorted(nodes.attribute_names):
if attr in categoricals:
enumeration = np.asarray(nodes.get_enumeration(attr, _all))
values = np.asarray(nodes.enumeration_values(attr))
# if the size of `values` is large enough compared to `enumeration`, not using
# categorical reduces the memory usage.
if values.shape[0] < 0.5 * enumeration.shape[0]:
result[attr] = pd.Categorical.from_codes(enumeration,
categories=values)
else:
result[attr] = values[enumeration]
else:
result[attr] = nodes.get_attribute(attr, _all)
for attr in sorted(
utils.add_dynamic_prefix(nodes.dynamics_attribute_names)):
result[attr] = nodes.get_dynamics_attribute(
attr.split(DYNAMICS_PREFIX)[1], _all)
return result
def _dynamics_params_names(self):
return set(
utils.add_dynamic_prefix(
self._population.dynamics_attribute_names))
def test_add_dynamic_prefix():
assert test_module.add_dynamic_prefix(
["a", "b"]) == [DYNAMICS_PREFIX + "a", DYNAMICS_PREFIX + "b"]
